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CHANGELOG.md

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wsidicom changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

0.22.0 - 2024-11-22

Added

  • Cache for compressed and decompressed tiles.
  • Setting strict_tile_size_check, defaulting to True, to enable parsing of levels with different tile size.

Changed

  • Default to placing the image at the middle of the slide if no TotalPixelMatrixOriginSequence is set when producing DICOM metadata .
  • Use Unix epoch as default datetime when producing DICOM metadata.
  • Group instances to pyramids with a configurable threshold to allow small differences in TotalPixelMatrixOriginSequence.

Fixed

  • Parsing of native pixel data with padded lenght.
  • Check for supported transfer syntax when DICOMWeb client returns an iterable of frames.
  • Fix for order of transfer syntax to check.
  • Use ImageType DERIVED instead of ORIGINAL when saving resampled volume instances.
  • Thread-safe parsing of pixel data frame index.

0.21.4 - 2024-10-30

Fixed

  • Loading of files with missing TotalPixelMatrixOriginSequence.

0.21.3 - 2024-10-28

Fixed

  • Missing WholeSlideMicroscopyImageFrameTypeSequence in produced DICOM dataset for some image types.
  • Do not insert empty ContainerComponentSequence and PrimaryAnatomicStructureSequence into produced DICOM dataset.
  • Only insert SpacingBetweenSlices into produced DICOM dataset if multiple focal planes.
  • Prefer use of ZOffsetInSlideCoordinateSystem in main DICOM dataset to attribute in SharedFunctionalGroupsSequence/PlanePositionSlideSequence.

0.21.2 - 2024-10-21

Fixed

  • Unpinned requirement for numpy to support numpy 2.

0.21.1 - 2024-10-17

Fixed

  • Restricted imagecodecs to exclude version 2024.9.22 due failing bug when encoding jpeg.

0.21.0 - 2024-10-08

Added

  • Support for pydicom 3.0. This requires Pyhton >3.10.

Removed

  • Support for Python 3.9.
  • Support for pydicom <3.

Fixed

  • Missing support for using fsspec in some methods.

0.20.6 - 2024-09-12

Fixed

  • Fixed version of pydicom to <3.0 to avoid breaking changes.

0.20.5 - 2024-07-25

Fixed

  • Removed debug printing.

0.20.4 - 2024-03-25

Fixed

  • Error when calculating downscaled image size causing save() with add_missing_levels to fail.
  • Missing sort when creating new pyramid levels, causing new levels to be created from a to high resolution level.

0.20.3 - 2024-03-20

Fixed

  • Missing handling of pyramid index when creating WsiInstance using create_instance().

0.20.2 - 2024-03-18

Fixed

  • Fixed handling of string values longer than allowed by value representation.
  • Corrected staining substances to be either a single string or a list of codes instead of a list of strings or codes.
  • Added allow_none for json metadata fields where it was missing.
  • Do not add empty CodingSchemeVersion to concept code name.

0.20.1 - 2024-02-22

Fixed

  • Changed default for parameter source_owned in __init__ of WsiDicom to be True, to by default close opened file handles.

0.20.0 - 2024-02-21

Added

  • Support for opening files using fsspec.
  • Support for reading tile offset from TIFF tags if dual DICOM TIFF file.

Fixed

  • Matching of slide uids between groups when validating opened instances.
  • Handling of missing dataset values if no default value.
  • Wrong concept name used when serializing and deserializing DICOM specimen samplings.

0.19.1 - 2024-02-14

Fixed

  • Correct handling of missing image coordinate system when loading metadata.

0.19.0 - 2024-02-12

Added

  • Support for decoding HT-JPEG2000 using Pillow, imagecodecs and/or pylibjpeg-openjpeg.
  • Optional codec pyjpegls for JPEG-LS support.

Fixed

  • Handling of non-conformant DICOM Web responses.

0.18.3 - 2024-01-22

Fixed

  • Fixed missing levels property.

0.18.2 - 2024-01-12

Fixed

  • Missing KeyError in exception catch for Pyramid.get(), that made getting image data for non-existing levels (by downscaling) not work.
  • Handle loading metadata if ExtendedDepthOfField not set.
  • Metadata for pyramid is now lazy loaded.

0.18.1 - 2024-01-12

Fixed

  • Missing indentation in Patient and Equipment metadata classes.

0.18.0 - 2024-01-12

Added

  • Models for DICOM WSI metadata.
  • Serializers from DICOM WSI to and from DICOM and json.
  • Support for multiple pyramids within the same slide. A pyramid must have the same image coordinate system and extended depth of field (if any). Use the pyramid-parameter to set the pyramid in for example read_region(), or use set_selected_pyramid() to set the pyramid to use. By default the first detected pyramid is used.
  • RLE encoding using image codecs.
  • JPEG 2000 encoding of lossless YBR using image codecs.

Changed

  • Levels with different extended depth of fields are no longer considered to be the same pyramid.

Removed

  • OpticalManager, replaced by new metadata model.

0.17.0 - 2023-12-10

Added

  • Option to not include label and overview in save().

Changed

  • Moved option to change label from open() to save().

0.16.0 - 2023-12-07

Added

  • Option to transcode when saving.
  • Option to limit levels to save.
  • Fallback to extended offset table if basic offset table is overflown.
  • Setting for what Pillow filter to use when scaling.
  • RGB support for Jpeg LS.

Changed

  • Refactored frame index reading (basic, extended, and no offset table and native pixel data) and table writing (basic and extended offset table).
  • Refactored methods for getting multiple tiles for ImageData to make it easier to implement more efficient methods.

0.15.2 - 2023-12-01

Fixed

  • Pillow handling of 16 bit grayscale images as 32 bit instead of 8 bit.
  • Using Pillow instead of Codec to decode frames from DICOM web, resulting in PIL.UnidentifiedImageError for transfer syntaxes not supported by Pillow.
  • Fix decoding of non-square images with PydicomDecoder and PylibjpegRleDecoder.

0.15.1 - 2023-11-30

Fixed

  • Correct order of pixel spacing.
  • Correct photometric_interpretation for Jpeg2kSettings
  • PillowEncoder encoding Jpeg2000 as Jpeg2kEncoder.

0.15.0 - 2023-11-30

Added

  • Fallback to EOT when overflowing BOT.
  • Use AvailableTransferSyntaxUID if provided to determine transfer syntax to use when opening DICOM Web instances.

Fixed

  • Missing empty BOT when writing EOT.
  • Fixed accessing settings for PillowEncoder.

0.14.0 - 2023-11-29

Added

  • Support for additional transfer syntaxes both for reading and writing, using pydicom pixel handlers, (optional) image codecs, and (optional) pylibjpeg-rle.
  • Additional decoders and encoders to Pillow. Decoder and encoder is selected automatically. Decoder to use can be overridden with the prefered_decoder-setting.
  • Detection of suitable available transfer syntax when opening slide with DICOM web.
  • Support for opening DICOMDIR files using open_dicomdir().

Changed

  • Opening DICOM web instances in parallel. Configurable with open_web_theads-setting.
  • open_web() now takes a list of requested transfer syntaxes to test if available from the server.
  • When fetching multiple frames from DICOM web, fetch multiple frames per request instead of making several requests.
  • Renamed OffsetTableType option NONE to EMPTY, and added type NONE for use with unencapsulated data.

Removed

  • Support for Python 3.8.

Fixed

  • Loading annotation instances using DICOM web.

0.13.0 - 2023-11-11

Added

  • Allow a requests.Session object to be passed to WsiDicomWebClient.create_client().

Changed

  • Refactored WsiDicomWebClient.__init__() to take a DICOMwebClient instance, and moved the old __init__() method into WsiDicomWebClient.create_client().
  • Make some arguments optional for WsiDicomWebClient.create_client().
  • Removed WsiDicomFileClient since it is no longer needed.
  • Fetching multiple frames in one request instead of one request per frame when using DICOM Web.
  • Allow multiple series UIDs to be passed to WsiDicom.open_web().
  • Loosen UID matching to just study_instance.
  • Require equality of 'TotalPixelMatrixOriginSequence' when matching datasets.

0.12.0 - 2023-10-04

Changed

  • Updated dependency of Pillow to include Pillow 10.
  • Tests written as pytests instead of unittest.

0.11.0 - 2023-08-09

Added

  • Override image size for labels and overviews if it is likely to be wrong.

Changed

  • Use logger instead of issuing warnings.

Fixed

  • Error in documentation of read_overview() in readme.
  • Spellings.

0.10.0 - 2023-06-01

Added

  • Support for using opened streams.

Changed

  • Consider image as full tiled if only one tile.

Removed

  • CidConceptCode.from_meaning(), use constructor with only meaning instead.

Fixed

  • Correct formatting of decimal string values when writing dataset.

0.9.0 - 2023-03-31

Added

  • Support for opening DICOM WSI using DICOMWeb.
  • save() now takes the optional parameter add_missing_levels, that enables adding missing pyramid levels up to the single-tile level.
  • read_region(), read_region_mm(), and read_region_mpp() takes an optional parameter threads, that allows multiple threads to be used for stitching together the region.

Changed

  • WsiDicom is now initialized using a Source, that is responsible for provides the instances to view.
  • Saving a WsiDicom is now handled by WsiDicomFileTarget.
  • Refactoring due to adding support for DICOMWeb and opening instances using Source and saving using Target.
  • Frame positions and tiling for levels are now parsed lazily, e.g. on first tile access.

Removed

  • The construct_pyramid() method of the Levels-class has been removed in favour of the add_missing_levels-parameter in save()

0.8.0 - 2023-03-21

Added

  • Set TotalPixelMatrixOriginSequence and ImageOrientationSlide from ImageOrgin object.

0.7.0 - 2023-02-13

Added

  • Parameter to change label to given image.

Changed

  • Label and overview series can now be None.

0.6.0 - 2023-01-24

Changed

  • Raise WsiDicomNotFoundError if no files found for open().
  • Added Python 3.11 as supported version.

0.5.0 - 2022-12-13

Added

  • Method to center-zoom a Region or RegionMm.

Changed

  • Do not use threads in method WsiDicomFileWriter._write_pixel_data() if only one worker.

0.4.0 - 2022-06-30

Added

  • Focal planes are considered equal if configurable within threshold distance, see config.focal_plane_distance_threshold
  • Option to read region defined in slide coordinate system for get_region_mm().

Changed

  • Default chunk size for saving is now set to 16 tiles.
  • Drop support for python 3.7.

Fixed

  • Focal planes are now written to file in correct order.

0.3.2 - 2022-05-08

Fixed

  • Fix version in init.py.

0.3.2 - 2022-05-08

Fixed

  • Fix version in init.py

0.3.1 - 2022-05-04

Fixed

  • Order of parameters for ConceptCode matches pydicom Code.

0.3.0 - 2022-04-20

Added

  • Simple check for if DICOM WSI is formatted for fast viewing (WsiDicom.ready_for_viewing()).
  • version added.

Changed

  • Action for downloading test data.
  • Do not set pydicom configuration parameters.

Fixed

  • Use correct data type for 32 bit integer in numpy arrays.
  • Fix check for if focal planes are sparse.

0.2.0 - 2022-02-14

Added

  • Configuration through global variable settings.
  • Relaxed requirements for some DICOM attributes.
  • Writing BOT and EOT, and reading EOT.
  • Pyramid creation.

Changed

  • save() converts the dataset to TILED_FULL.

Removed

  • Using null path as output path for save().

Fixed

  • Fix NumberOfFrames when saving.

0.1.0 - 2021-11-26

Added

  • Initial release of wsidicom